rs13219181

Variant names:

• chr6-27168446-A-G
• rs13219181

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.14 in 152,212 control chromosomes in the GnomAD database, including 1,631 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.14 (1631 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127
• Publications: 17 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21270 AN: 152092 Hom.: 1631 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0827

Gnomad EAS AF: 0.00852

Gnomad SAS AF: 0.0935

Gnomad FIN AF: 0.0901

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.126

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.140 AC: 21270 AN: 152212 Hom.: 1631 Cov.: 32 AF XY: 0.133 AC XY: 9914 AN XY: 74442

African (AFR) AF: 0.141 AC: 5871 AN: 41536

American (AMR) AF: 0.107 AC: 1633 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0827 AC: 287 AN: 3472

East Asian (EAS) AF: 0.00854 AC: 44 AN: 5150

South Asian (SAS) AF: 0.0921 AC: 445 AN: 4830

European-Finnish (FIN) AF: 0.0901 AC: 956 AN: 10608

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11540 AN: 68004

Other (OTH) AF: 0.124 AC: 262 AN: 2108

Alfa AF: 0.160 Hom.: 631

Bravo AF: 0.142

Asia WGS AF: 0.0590 AC: 206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.69
PhyloP100		0.13

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs13219181; hg19: chr6-27136225;